Running my fasta_output parser f2b.pl

The SP's usage policy restricts interactive jobs to less than 20 mins. So if you have a huge fasta-result file to parse out (using my f2b.pl or otherwise), you'd be better off submitting the job through the load leveller (LL) job submission tool. The LL needs you to write short shell scripts specifying various parameters like output filename, class of the job, etc.

Here's a sample script which submits a class 'a' job to execute f2b.pl. Note how the output and error filenames are specified and also how they are linked to the job using $(Cluster)..

The above test run should create a `myfile.fasta_all_all.bagin' in /gpfs/agopu/. It should also create an output file (and an error file if there were errors down the line) of the form `sample_llscript.<job_id<.out' (Example: sample_llscript.10820.out).

For more details about LL scripts, jobs statuses and such, please look at the SP section of the RATS manual webpages; it has excellent documentation on a lot of associated issues. For information on various computing resources available to IU scientists and students (with faculty sponsorship in certain cases), visit the RAC home page and the supercomputers page.